Genome-Wide Association Study Identifies Genomic Regions for Important Morpho-Agronomic Traits in Mesoamerican Common Bean

Jessica Delfini; Vânia Moda-Cirino; José Dos Santos Neto; Douglas Mariani Zeffa; Alison Fernando Nogueira; Luriam Aparecida Brandão Ribeiro; Paulo Maurício Ruas; Paul Gepts; Leandro Simões Azeredo Gonçalves

doi:10.3389/fpls.2021.748829

Genome-Wide Association Study Identifies Genomic Regions for Important Morpho-Agronomic Traits in Mesoamerican Common Bean

Front Plant Sci. 2021 Oct 7:12:748829. doi: 10.3389/fpls.2021.748829. eCollection 2021.

Authors

Affiliations

¹ Área de Genética e Melhoramento Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Brazil.
² Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Brazil.
³ Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Brazil.
⁴ Departamento de Biologia, Universidade Estadual de Londrina, Londrina, Brazil.
⁵ Section of Crop and Ecosystem Sciences, Department of Plant Sciences, University of California, Davis, Davis, CA, United States.

Abstract

The population growth trend in recent decades has resulted in continuing efforts to guarantee food security in which leguminous plants, such as the common bean (Phaseolus vulgaris L.), play a particularly important role as they are relatively cheap and have high nutritional value. To meet this demand for food, the main target for genetic improvement programs is to increase productivity, which is a complex quantitative trait influenced by many component traits. This research aims to identify Quantitative Trait Nucleotides (QTNs) associated with productivity and its components using multi-locus genome-wide association studies. Ten morpho-agronomic traits [plant height (PH), first pod insertion height (FPIH), number of nodules (NN), pod length (PL), total number of pods per plant (NPP), number of locules per pod (LP), number of seeds per pod (SP), total seed weight per plant (TSW), 100-seed weight (W100), and grain yield (YLD)] were evaluated in four environments for 178 Mesoamerican common bean domesticated accessions belonging to the Brazilian Diversity Panel. In order to identify stable QTNs, only those identified by multiple methods (mrMLM, FASTmrMLM, pLARmEB, and ISIS EM-BLASSO) or in multiple environments were selected. Among the identified QTNs, 64 were detected at least thrice by different methods or in different environments, and 39 showed significant phenotypic differences between their corresponding alleles. The alleles that positively increased the corresponding traits, except PH (for which lower values are desired), were considered favorable alleles. The most influenced trait by the accumulation of favorable alleles was PH, showing a 51.7% reduction, while NN, TSW, YLD, FPIH, and NPP increased between 18 and 34%. Identifying QTNs in several environments (four environments and overall adjusted mean) and by multiple methods reinforces the reliability of the associations obtained and the importance of conducting these studies in multiple environments. Using these QTNs through molecular techniques for genetic improvement, such as marker-assisted selection or genomic selection, can be a strategy to increase common bean production.

Keywords: GWAS—genome-wide association study; Phaseolus vulgaris L.; favorable alleles; genetic improvement; yield.